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Background  WRKY III genes have significant functions in regulating plant development and resistance. In plant, WRKY gene family has been studied in many species, however, there still lack a comprehensive analysis of WRKY III genes in the woody plant species poplar, three representative lineages of flowering plant species are incorporated in most analyses:  Arabidopsis  (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots) and  Oryza sativa  (a model plant for monocots).    Results  In this study, we identified 10, 6, 13 and 28 WRKY III genes in the genomes of  Populus trichocarpa , grape ( Vitis vinifera ),  Arabidopsis thaliana  and rice ( Oryza sativa ), respectively. Phylogenetic analysis revealed that the WRKY III proteins could be divided into four clades. By microsynteny analysis, we found that the duplicated regions were more conserved between poplar and grape than  Arabidopsis  or rice. We dated their duplications by Ks analysis of  Populus  WRKY III genes and demonstrated that all the blocks were formed after the divergence of monocots and dicots. Strong purifying selection has played a key role in the maintenance of WRKY III genes in  Populus . Tissue expression analysis of the WRKY III genes in  Populus  revealed that five were most highly expressed in the xylem. We also performed quantitative real-time reverse transcription PCR analysis of WRKY III genes in  Populus  treated with salicylic acid, abscisic acid and polyethylene glycol to explore their stress-related expression patterns.    Conclusions  This study highlighted the duplication and diversification of the WRKY III gene family in  Populus  and provided a comprehensive analysis of this gene family in the  Populus  genome. Our results indicated that the majority of WRKY III genes of  Populus  was expanded by large-scale gene duplication. The expression pattern of  PtrWRKYIII  gene identified that these genes play important roles in the xylem during poplar growth and development, and may play crucial role in defense to drought stress. Our results presented here may aid in the selection of appropriate candidate genes for further characterization of their biological functions in poplar.    Reviewers  This article was reviewed by Prof Dandekar and Dr Andrade-Navarro.    Electronic supplementary material  The online version of this article (doi:10.1186/s13062-015-0076-3) contains supplementary material, which is available to authorized users.

Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice